elasticsearch: Clear tool output before indexing

This is both huge, and difficult to normalize for Elasticsearch.

Fixes #7038.
bagit: shorten argument list

Fixes #6624
bagit: remove orphaned sip_dir variable

refs #6624
Update ffmpeg MKV normalization command

* Correct ffmpeg FPTool version
* Use FFV1 level 3
* Correctly normalize files with anything other than 1:1 video/audio
  stream counts

Fixes #5496
FITS: use nailgun

refs #5509
FPR: add Tesseract command and rules

refs #6565
createMETS2: prefix PREMIS elements

Leaving PREMIS elements unprefixed resulted in any other unprefixed
elements being interpreted as being PREMIS - for example, un-namespaced
documents from external sources.

Fixes #7055.
Print exception message instead of sys.exc_info
Metadata processing: Add file ID, characterization

refs #6575

Metadata files should have identification and characterization information
in the METS file. Add those microservices to metadata processing. Update
processing config to reflect this. Fix a couple microservice group
discontinuities.
Update createStructuredDirectory

Move createStructuredDirectory into archivematicaFunctions and rename
create_structured_directory so it can take advantage of the directory
constants and functions already there.  Add manual normalization
constants to that file as well.  Update all callers, remove now
deprecated archivematicaCreateStructuredDirectory.py/sh, and do some
minor cleanup.
Add AIP reingest button

refs #6488

Add Reingest button to the archival storage tab which POSTs to the
storage service reingest endpoint.  Add reingest form and storage
service helper to support this
Initial updates for Re-ingest AIP

refs #6488

Reuse existing DIP from AIP MSCLs and update for newer, more general use
case.

Update determineAIPVersionKeyExitCode to default to the only path
available, as there are no exceptions to AIP processing currently.
Remove assignFauxFileUUIDs and renameDIPFauxToOrigUUIDs as we won't be
using fake IDs to separate the original SIP from the reingested AIP.

Many SQL updates:
* Fix typos, remove bizarre links
* Update microservice groups to make them more contiguous
* Verify checksums moved to after metadata processing, as metadata
generates checksums too
* Metadata reminder moved to before submission documentation and
metadata processed
* Remove old style file ID
* Update reingest chain to use existing DIP and AIP creation, instead
of custom path
* Add processingMCP to reingest path
* Remove useless magic link, clean up setup for normalization and
setting which normalization node to go to
* Delete all TasksConfigs and StandardTasksConfigs that have no foreign
keys pointing at them
Rename DIPfromAIP to reingest AIP

refs #6488

Rename MicroServiceChainLinks and watched directory to reflect actual
purpose.
MCPServer sets currentPath in watchedDirectories

When starting a chain from a watched directory, ensure a SIP's
current path matches the one found in the directory.  This can happen
during AIP reingest, where the last know location is not the watched
directory it is currently in. Do not change currentPath for DIPs, as
they can run in parallel with the originating SIP and overwrite the
SIP's information. Also, some cleanup.
Entry filter in browse is configurable

The filter to determine which files/folders are displayed when browsing the
storage service (ie starting a transfer) is now a parameter, instead of
builtin.  Default is still to display folders but not files.
Stub of add metadata files

wip
Fill in add metadata files

squash with above and add better commit message later
Post API information to storage service

If default setup requested, post the initial user and API key to the
storage service when registering.
Add start reingest endpoint

refs #6488

Add start reingest endpoint to move the new SIP from tmp to the reingest
watched directory.  This is where any pre-processing will happen, such as
clearing remnants of the old SIP from the DB.

Update helpers.json_response to accept a status code to pass to the
response.
Handle failed reingest

refs #6488

Update reject reingest to use normal rejected SIP chain.  Rejected or
failed SIPS attempt to reset their ingest status with the storage service.
Display errors from the storage service properly when starting reingest.